The Pikmin games have a variety of controls used to control the game's menus, leaders, camera and gameplay mechanics. These controls come in the form of button presses and releases, analog stick tilts, Wii Remote pointer movements and touchscreen touches.

For the GameCube games, there are two button combinations that replace the need to interact with the physical console itself: one resets the game without pressing the button on the console, and the other resets the controller's neutral position, without needing to unplug and replug it. The former can be achieved by holding + + for a few seconds. For the latter, the player must hold + + , for three seconds, without touching , , or . This is because when the console is booted, or the controller's neutral position is reset, the position of the sticks and the analog shoulder buttons is considered to be the default. If, for instance, the Control Stick is held to the right when the default position is being registered, then the game will assume that the Stick is being held left, if the player releases the Control Stick.

The term button-mashing is used when a player rapidly presses buttons or tilts sticks on the controller, without any discernible pattern. The point of doing this varies between games and scenarios, but in the Pikmin games, one may have to button-mash in certain situations in order to achieve a goal. The following situations require the player to button-mash:

When the current leader is being attacked by an opposing Pikmin, twirling the main analog stick allows the leader to shake them off; they'll remained latched until the stick is twirled for long enough. In Pikmin and New Play Control! Pikmin, actual buttons can also be pressed rapidly to shake off Mushroom Pikmin.

In Pikmin 3, when a leader is thrown to the ground, the player can mash directions on / – such as twirling – to make them get up. The player can also shake the Nunchuk to make them get up (usually easier and faster). The leader will get up by themselves eventually, however.

In a sense, it could be said that the games prior to Pikmin 3 require the player to mash / to continuously pluck Pikmin, but this is only partially true: the player needs only to press the button during a pluck animation, in order to assure that the next Pikmin will also be automatically plucked. In addition, mashing the throw button is required in order to throw Pikmin in quick succession.

If the player is not interested in a cutscene's dialog, the fastest way to advance it is by mashing the / / and / / buttons. If the game in question allows using the "B" button to both advance the text and auto-fill the letters, then that button may be mashed alone.

Move Pikmin group. They will go to a task if they bump into an object and they will no longer be on the party. In the New Play Control! version, the Pikmin will go to wherever the cursor is, when the button is held down.

The sequel retains many of the controls from the first game, but with some additions and changes. Like the first game, the original GameCube version is played using a GameCube controller, while the New Play Control! Pikmin 2 version is played with the Wii Remote.

GameCube

Wii

Action

While commanding Pikmin: Pick a Pikmin up. When the button is released, the leader throws the Pikmin.

Whistle. Holding it down longer increases the range. Any Pikmin caught in the whistle will come to the leader's command. The Mega Tweeter increases the range of the whistle by 1.5 times. If the Pluckaphone has been collected, any sprouts will come out, too.

(Fully held)

Move in the direction it is held. If a Pikmin is touched while running, it will join the leader. The leaders run as fast as a flower Red/Blue/Yellow Pikmin, and with the Rush Boots, as fast as a flower White Pikmin.

Move Pikmin group. They will go to a task if they bump into an object and they will no longer be on the party. In the New Play Control! version, the Pikmin will go to wherever the cursor is, when the button is held down.

Pikmin 3 allows for four ways to control the game. The player can use the the GamePad's buttons, the Wii Remote + Nunchuk, the Wii U Pro Controller, or, as of version 2.0.0, the GamePad's touchscreen; the latter is known as "Stylus Mode". The Wii Classic Controller is not supported. When the player uses a control from a controller different from the one they're currently using, a message will appear on-screen saying the main controller has changed, and the player is then allowed to use that controller from there on out. The exception to this is .

In addition, the player can toggle Off-TV Play with . While Off-TV Play mode is on, the TV screen will display some Pikmin moving from right to left on a black screen, with the message "Look at the GamePad." on the bottom. Given that with Off-TV Play off, the player uses the TV screen as the main gameplay view-port and the GamePad as the radar, the player will need to use to toggle between gameplay view and radar view, if Off-TV Play is on.

If the player wishes to play with the Wii Remote and Off-TV Play, they must point the Wii Remote at the GamePad, as opposed to the Sensor Bar.

Move in the direction it is held. If a Pikmin is touched while running, it will join the leader. The leaders run a bit slower than flower Pikmin. With the Wii Remote, the camera will automatically rotate to make it easier to navigate.

With Stylus Mode, the player does the majority of the important actions by pressing on the touchscreen. If both Off-TV Play and Stylus Mode are enabled, the controls are exactly the same, and the same touchscreen spot maps to exactly the same game world location in both modes. To use an ultra-spicy spray, dismiss/charge, open the KopPad's apps, or switch leaders, the corresponding buttons on the left side of the touchscreen must be tapped.

GamePad

Action

At any time: Hold to enable whistling. If you tap or hold on the touch screen, you can whistle with held.

While commanding Pikmin: Tap to change which Pikmin type (or leader) will be thrown next. Won't take effect if you whistled after pressing.

When by a sprout: Release to pluck the Pikmin sprout out of the ground. Won't take effect if you whistled after pressing.

Without any Pikmin and near a punchable target: Release to punch. Won't take effect if you whistled after pressing.

When under an Onion: Release to open its menu. Won't take effect if you whistled after pressing.

Move in the direction it is held. If a Pikmin is touched while running, it will join the leader. The leaders run a bit slower than flower Pikmin. The camera will automatically rotate to make it easier to navigate.

Tap or hold to move the cursor to where the Stylus is. Move the cursor near the left and right borders of the screen to make the camera rotate horizontally. Tap the stylus on a location to throw Pikmin (or leaders) there, if you have any on the party. If the touchscreen is depressed and is held, whistles towards the touched location. Tap the icons on the left portion of the screen to use an ultra-spicy spray, dismiss/charge, use the KopPad's apps, or switch leaders.

If the cursor is on a target, toggles lock-on. Otherwise, press to make the camera face the same way the leader is facing.

In the first two games and the New Play Control! remakes, the Onion menu allows the player to withdraw or save Pikmin using a simple control interface.

Pressing up or down on the D-Pad or main Analog Stick of the controller allows the player to change the amount of Pikmin of that type in the party. Missing or excessive Pikmin will be automatically withdrawn or stored accordingly. Up increases the amount of Pikmin in the Onion, while down increases the amount in the group.

In Pikmin, due to the actions that can be performed by Pikmin carrying bomb rocks, some special notes need to be taken into consideration in order to not have a bomb-rock explode accidentally.

When a bomb rock Yellow Pikmin is thrown, it becomes in a standby state. By whistling this Pikmin, it drops its bomb rock, which begins its detonation timer. In order to safely retrieve the Pikmin without detonating the bomb rock, the Pikmin must be touched by the leader. Dismissed Pikmin that have not been thrown will always keep their bomb rock when returning to the party. Finally, any bomb rock-carrying Yellow Pikmin that is told to go into an Onion will drop the bomb rock safely by one of the Onion's legs.

In the first game, if the radar is opened, / can be used to flip to a different page, containing an illustration that maps the different buttons on the controller to the corresponding actions. This can be used should the player forget the controls.